diff --git a/config.yaml b/config.yaml index 7a0a6823..b38f16ce 100644 --- a/config.yaml +++ b/config.yaml @@ -3,7 +3,7 @@ ######################################################################################################################## # See https://www.rapids.science/latest/setup/configuration/#participant-files -PIDS: ['p031', 'p032', 'p033', 'p034', 'p035', 'p036', 'p037', 'p038', 'p039', 'p040', 'p042', 'p043', 'p044', 'p045', 'p046', 'p049', 'p050', 'p052', 'p053', 'p054', 'p055', 'p057', 'p058', 'p059', 'p060', 'p061', 'p062', 'p064', 'p067', 'p068', 'p069', 'p070', 'p071', 'p072', 'p073', 'p074', 'p075', 'p076', 'p077', 'p078', 'p079', 'p080', 'p081', 'p082', 'p083', 'p084', 'p085', 'p086', 'p088', 'p089', 'p090', 'p091', 'p092', 'p093', 'p106', 'p107'] +PIDS: ['p01'] # See https://www.rapids.science/latest/setup/configuration/#automatic-creation-of-participant-files CREATE_PARTICIPANT_FILES: @@ -685,14 +685,14 @@ ALL_CLEANING_INDIVIDUAL: CORR_THRESHOLD: 0.95 SRC_SCRIPT: src/features/all_cleaning_individual/rapids/main.R STRAW: # currently the same as RAPIDS provider with a change in selecting the imputation type - COMPUTE: False + COMPUTE: True IMPUTE_PHONE_SELECTED_EVENT_FEATURES: COMPUTE: False TYPE: median # options: zero, mean, median or k-nearest MIN_DATA_YIELDED_MINUTES_TO_IMPUTE: 0.33 COLS_NAN_THRESHOLD: 0.3 # set to 1 to disable COLS_VAR_THRESHOLD: True - ROWS_NAN_THRESHOLD: 0 # set to 1 to disable + ROWS_NAN_THRESHOLD: 1 # set to 1 to disable DATA_YIELD_FEATURE: RATIO_VALID_YIELDED_HOURS # RATIO_VALID_YIELDED_HOURS or RATIO_VALID_YIELDED_MINUTES DATA_YIELD_RATIO_THRESHOLD: 0 # set to 0 to disable DROP_HIGHLY_CORRELATED_FEATURES: @@ -705,7 +705,7 @@ ALL_CLEANING_OVERALL: CLEAN_STANDARDIZED: True PROVIDERS: RAPIDS: - COMPUTE: False + COMPUTE: True IMPUTE_SELECTED_EVENT_FEATURES: COMPUTE: False MIN_DATA_YIELDED_MINUTES_TO_IMPUTE: 0.33 @@ -720,14 +720,14 @@ ALL_CLEANING_OVERALL: CORR_THRESHOLD: 0.95 SRC_SCRIPT: src/features/all_cleaning_overall/rapids/main.R STRAW: # currently the same as RAPIDS provider with a change in selecting the imputation type - COMPUTE: False + COMPUTE: True IMPUTE_PHONE_SELECTED_EVENT_FEATURES: COMPUTE: False TYPE: median # options: zero, mean, median or k-nearest MIN_DATA_YIELDED_MINUTES_TO_IMPUTE: 0.33 COLS_NAN_THRESHOLD: 0.3 # set to 1 to disable COLS_VAR_THRESHOLD: True - ROWS_NAN_THRESHOLD: 0 # set to 1 to disable + ROWS_NAN_THRESHOLD: 1 # set to 1 to disable DATA_YIELD_FEATURE: RATIO_VALID_YIELDED_HOURS # RATIO_VALID_YIELDED_HOURS or RATIO_VALID_YIELDED_MINUTES DATA_YIELD_RATIO_THRESHOLD: 0 # set to 0 to disable DROP_HIGHLY_CORRELATED_FEATURES: @@ -759,7 +759,7 @@ STANDARDIZATION: # Standardization for both providers is executed if only one of PARAMS_FOR_ANALYSIS: BASELINE: - COMPUTE: True + COMPUTE: False FOLDER: data/external/baseline CONTAINER: [results-survey637813_final.csv, # Slovenia results-survey358134_final.csv, # Belgium 1 @@ -770,5 +770,5 @@ PARAMS_FOR_ANALYSIS: CATEGORICAL_FEATURES: [gender] TARGET: - COMPUTE: True + COMPUTE: False LABEL: PANAS_negative_affect_mean diff --git a/src/features/all_cleaning_individual/rapids/main.R b/src/features/all_cleaning_individual/rapids/main.R index 1d1636c2..751dc64b 100644 --- a/src/features/all_cleaning_individual/rapids/main.R +++ b/src/features/all_cleaning_individual/rapids/main.R @@ -39,8 +39,10 @@ rapids_cleaning <- function(sensor_data_files, provider){ if(!data_yield_column %in% colnames(clean_features)){ stop(paste0("Error: RAPIDS provider needs to clean data based on ", data_yield_column, " column, please set config[PHONE_DATA_YIELD][PROVIDERS][RAPIDS][COMPUTE] to True and include 'ratiovalidyielded", data_yield_unit, "' in [FEATURES].")) } - clean_features <- clean_features %>% + if (data_yield_ratio_threshold > 0) { + clean_features <- clean_features %>% filter(.[[data_yield_column]] >= data_yield_ratio_threshold) + } # Drop columns with a percentage of NA values above cols_nan_threshold if(nrow(clean_features)) diff --git a/src/features/all_cleaning_individual/straw/main.py b/src/features/all_cleaning_individual/straw/main.py index f82a355d..6ba3ba5e 100644 --- a/src/features/all_cleaning_individual/straw/main.py +++ b/src/features/all_cleaning_individual/straw/main.py @@ -36,7 +36,8 @@ def straw_cleaning(sensor_data_files, provider): if not data_yield_column in features.columns: raise KeyError(f"RAPIDS provider needs to impute the selected event features based on {data_yield_column} column, please set config[PHONE_DATA_YIELD][PROVIDERS][RAPIDS][COMPUTE] to True and include 'ratiovalidyielded{data_yield_unit}' in [FEATURES].") - features = features[features[data_yield_column] >= provider["DATA_YIELD_RATIO_THRESHOLD"]] + if provider["DATA_YIELD_RATIO_THRESHOLD"]: + features = features[features[data_yield_column] >= provider["DATA_YIELD_RATIO_THRESHOLD"]] esm_cols = features.loc[:, features.columns.str.startswith('phone_esm')] # For later preservation of esm_cols diff --git a/src/features/all_cleaning_overall/rapids/main.R b/src/features/all_cleaning_overall/rapids/main.R index 6221c428..b3b7284d 100644 --- a/src/features/all_cleaning_overall/rapids/main.R +++ b/src/features/all_cleaning_overall/rapids/main.R @@ -39,8 +39,10 @@ rapids_cleaning <- function(sensor_data_files, provider){ if(!data_yield_column %in% colnames(clean_features)){ stop(paste0("Error: RAPIDS provider needs to clean data based on ", data_yield_column, " column, please set config[PHONE_DATA_YIELD][PROVIDERS][RAPIDS][COMPUTE] to True and include 'ratiovalidyielded", data_yield_unit, "' in [FEATURES].")) } - clean_features <- clean_features %>% + if (data_yield_ratio_threshold > 0) { + clean_features <- clean_features %>% filter(.[[data_yield_column]] >= data_yield_ratio_threshold) + } # Drop columns with a percentage of NA values above cols_nan_threshold if(nrow(clean_features)) diff --git a/src/features/all_cleaning_overall/straw/main.py b/src/features/all_cleaning_overall/straw/main.py index f82a355d..6ba3ba5e 100644 --- a/src/features/all_cleaning_overall/straw/main.py +++ b/src/features/all_cleaning_overall/straw/main.py @@ -36,7 +36,8 @@ def straw_cleaning(sensor_data_files, provider): if not data_yield_column in features.columns: raise KeyError(f"RAPIDS provider needs to impute the selected event features based on {data_yield_column} column, please set config[PHONE_DATA_YIELD][PROVIDERS][RAPIDS][COMPUTE] to True and include 'ratiovalidyielded{data_yield_unit}' in [FEATURES].") - features = features[features[data_yield_column] >= provider["DATA_YIELD_RATIO_THRESHOLD"]] + if provider["DATA_YIELD_RATIO_THRESHOLD"]: + features = features[features[data_yield_column] >= provider["DATA_YIELD_RATIO_THRESHOLD"]] esm_cols = features.loc[:, features.columns.str.startswith('phone_esm')] # For later preservation of esm_cols